A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Cheng, Tiejun ^a   Liu, Zhihai ^a   Wang, Renxiao ^a  

^a SHANGHAI INSTITUTE OF ORGANIC CHEMISTRY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURATE PREDICTION; AUTOMATIC ALGORITHMS; PHARMACOPHORE MODELING; PROTEIN-LIGAND BINDING AFFINITIES; PROTEIN-LIGAND COMPLEXES; PROTEIN-LIGAND INTERACTIONS; REPARAMETERIZATION; STRUCTURE-BASED DRUG DESIGN;

BINDING ENERGY; COMPLEXATION;

FORECASTING;

HUMAN IMMUNODEFICIENCY VIRUS;

LIGAND; PROTEIN;

ALGORITHM; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; DRUG DESIGN; METABOLISM; PROTEIN CONFORMATION; PROTEIN DATABASE; STRUCTURE ACTIVITY RELATION;

ALGORITHMS; BINDING SITES; DATABASES, PROTEIN; DRUG DESIGN; LIGANDS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 77950908360     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-193     Document Type: Article

References (73)

1. Lybrand TP. Ligand-Protein Docking and Rational Drug Design. Curr Opin Struct Biol 1995, 5(2):224-228. 10.1016/0959-440X(95)80080-8, 7648325.
2. Kollman PA. Theory of Macromolecule-Ligand Interactions. Curr Opin Struct Biol 1994, 4(2):240-245.
3. Fischer E. Einfluss der Configuration auf die Wirkung der Enzyme. Ber Dtsch Chem Ges 1894, 27:2985-2993.
4. McInnes C. Virtual Screening Strategies in Drug Discovery. Curr Opin Chem Biol 2007, 11(5):494-502. 10.1016/j.cbpa.2007.08.033, 17936059.
5. Shoichet BK. Virtual screening of chemical libraries. Nature 2004, 432(7019):862-865. 10.1038/nature03197, 1360234, 15602552.
6. Lyne PD. Structure-Based Virtual Screening: an Overview. Drug Discov Today 2002, 7(20):1047-1055. 10.1016/S1359-6446(02)02483-2, 12546894.
7. Walters WP, Stahl MT, Murcko MA. Virtual Screening - an Overview. Drug Discov Today 1998, 3:160-178.
8. Warren GL, Andrews CW, Capelli AM, Clarke B, LaLonde J, Lambert MH, Lindvall M, Nevins N, Semus SF, Senger S, et al. A Critical Assessment of Docking Programs and Scoring Functions. J Med Chem 2006, 49(20):5912-5931. 10.1021/jm050362n, 17004707.
9. Kellenberger E, Rodrigo J, Muller P, Rognan D. Comparative evaluation of eight docking tools for docking and virtual screening accuracy. Proteins: Struct, Funct, Bioinf 2004, 57(2):225-242.
10. Ewing TJA, Makino S, Skillman AG, Kuntz ID. DOCK 4.0: Search Strategies for Automated Molecular Docking of Flexible Molecule Databases. J Comput-Aided Mol Des 2001, 15(5):411-428. 10.1023/A:1011115820450, 11394736.
11. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ. Automated Docking Using a Lamarckian Genetic Algorithm and an Empirical Binding Free Energy Function. J Comput Chem 1998, 19(14):1639-1662.
12. Morris GM, Goodsell DS, Huey R, Olson AJ. Distributed Automated Docking of Flexible Ligands to Proteins: Parallel Applications of AutoDock 2.4. J Comput-Aided Mol Des 1996, 10(4):293-304. 10.1007/BF00124499, 8877701.
13. Goodsell DS, Olson AJ. Automated Docking of Substrates to Proteins by Simulated Annealing. Proteins: Struct, Funct, Genet 1990, 8(3):195-202.
14. Rarey M, Kramer B, Lengauer T, Klebe G. A Fast Flexible Docking Method Using an Incremental Construction Algorithm. J Mol Biol 1996, 261(3):470-489. 10.1006/jmbi.1996.0477, 8780787.
15. Jain A. Surflex-Dock 2.1: Robust Performance from Ligand Energetic Modeling, Ring Flexibility, and Knowledge-Based Search. J Comput-Aided Mol Des 2007, 21(5):281-306. 10.1007/s10822-007-9114-2, 17387436.
16. Jain AN. Surflex: Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine. J Med Chem 2003, 46(4):499-511. 10.1021/jm020406h, 12570372.
17. Venkatachalam CM, Jiang X, Oldfield T, Waldman M. LigandFit: A Novel Method for the Shape-Directed Rapid Docking of Ligands to Protein Active Sites. J Mol Graphics Modell 2003, 21(4):289-307.
18. Jones G, Willett P, Glen RC, Leach AR, Taylor R. Development and Validation of a Genetic Algorithm for Flexible Docking. J Mol Biol 1997, 267(3):727-748. 10.1006/jmbi.1996.0897, 9126849.
19. Jones G, Willett P, Glen RC. Molecular Recognition of Receptor Sites Using a Genetic Algorithm with a Description of Desolvation. J Mol Biol 1995, 245(1):43-53. 10.1016/S0022-2836(95)80037-9, 7823319.
20. Friesner RA, Murphy RB, Repasky MP, Frye LL, Greenwood JR, Halgren TA, Sanschagrin PC, Mainz DT. Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes. J Med Chem 2006, 49(21):6177-6196. 10.1021/jm051256o, 17034125.
21. Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, et al. Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy. J Med Chem 2004, 47(7):1739-1749. 10.1021/jm0306430, 15027865.
22. Cheng T, Li X, Li Y, Liu Z, Wang R. Comparative Assessment of Scoring Functions on a Diverse Test Set. J Chem Inf Model 2009, 49(4):1079-1093. 10.1021/ci9000053, 19358517.
23. Brewerton SC. The use of protein-ligand interaction fingerprints in docking. Curr Opin Drug Discovery Dev 2008, 11(3):356-364.
24. Ferrara P, Gohlke H, Price DJ, Klebe G, Brooks CL. Assessing Scoring Functions for Protein-Ligand Interactions. J Med Chem 2004, 47(12):3032-3047. 10.1021/jm030489h, 15163185.
25. Marsden PM, Puvanendrampillai D, Mitchell JBO, Glen RC. Predicting protein-ligand binding affinities: a low scoring game?. Org Biomol Chem 2004, 2:3267-3273. 10.1039/b409570g, 15534704.
26. Wang R, Lu Y, Fang X, Wang S. An Extensive Test of 14 Scoring Functions Using the PDBbind Refined Set of 800 Protein-Ligand Complexes. J Chem Inf Comput Sci 2004, 44(6):2114-2125.
27. Wang R, Lu Y, Wang S. Comparative Evaluation of 11 Scoring Functions for Molecular Docking. J Med Chem 2003, 46(12):2287-2303. 10.1021/jm0203783, 12773034.
28. Kollman P. Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. Chem Rev 1993, 93(7):2395-2417.
29. Jorgensen WL. Free Energy Calculations: A Breakthrough for Modeling Organic Chemistry in Solution. Acc Chem Res 1989, 22(5):184-189.
30. Carlson HA, Jorgensen WL. An Extended Linear Response Method for Determining Free Energies of Hydration. J Phys Chem 1995, 99(26):10667-10673.
31. Aqvist J, Medina C, Samuelsson J-E. A New Method for Predicting Binding Affinity in Computer-Aided Drug Design. Protein Eng 1994, 7(3):385-391. 10.1093/protein/7.3.385, 8177887.
32. Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, et al. Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models. Acc Chem Res 2000, 33(12):889-897. 10.1021/ar000033j, 11123888.
33. Zhang X, Li X, Wang R. Interpretation of the Binding Affinities of PTP1B Inhibitors with the MM-GB/SA Method and the X-Score Scoring Function. J Chem Inf Model 2009, 49(4):1033-1048. 10.1021/ci8004429, 19320460.
34. Krammer A, Kirchhoff PD, Jiang X, Venkatachalam CM, Waldman M. LigScore: A Novel Scoring Function for Predicting Binding Affinities. J Mol Graphics Modell 2005, 23(5):395-407.
35. Wang R, Lai L, Wang S. Further Development and Validation of Empirical Scoring Functions for Structure-Based Binding Affinity Prediction. J Comput-Aided Mol Des 2002, 16(1):11-26. 10.1023/A:1016357811882, 12197663.
36. Wang R, Liu L, Lai L, Tang Y. SCORE: A New Empirical Method for Estimating the Binding Affinity of a Protein-Ligand Complex. J Mol Model 1998, 4(12):379-394.
37. Gehlhaar DK, Bouzida D, Rejto PA, . eds Rational Drug Design: Novel Methodology and Practical Applications. 1999, American Chemical Society: Washington DC, eds.
38. Gehlhaar DK, Verkhivker GM, Rejto PA, Sherman CJ, Fogel DR, Fogel LJ, Freer ST. Molecular Recognition of the Inhibitor AG-1343 by HIV-1 Protease: Conformationally Flexible Docking by Evolutionary Programming. Chem Biol 1995, 2(5):317-324. 10.1016/1074-5521(95)90050-0, 9383433.
39. Baxter CA, Murray CW, Clark DE, Westhead DR, Eldridge MD. Flexible Docking Using Tabu Search and an Empirical Estimate of Binding Affinity. Proteins: Struct, Funct, Genet 1998, 33(3):367-382.
40. Eldridge MD, Murray CW, Auton TR, Paolini GV, Mee RP. Empirical Scoring Functions: I. The Development of a Fast Empirical Scoring Function to Estimate the Binding Affinity of Ligands in Receptor Complexes. J Comput-Aided Mol Des 1997, 11(5):425-445. 10.1023/A:1007996124545, 9385547.
41. Jain AN. Scoring Noncovalent Protein-Ligand Interactions: A Continuous Differentiable Function Tuned to Compute Binding Affinities. J Comput-Aided Mol Des 1996, 10(5):427-440. 10.1007/BF00124474, 8951652.
42. Böhm H-J. Prediction of Binding Constants of Protein Ligands: A Fast Method for the Prioritization of Hits Obtained from de novo Design or 3D Database Search Programs. J Comput-Aided Mol Des 1998, 12(4):309-323. 10.1023/A:1007999920146, 9777490.
43. Böhm H-J. The Development of a Simple Empirical Scoring Function to Estimate the Binding Constant for a Protein-Ligand Complex of Known Three-Dimensional Structure. J Comput-Aided Mol Des 1994, 8(3):243-256. 10.1007/BF00126743, 7964925.
44. Mooij WTM, Verdonk ML. General and Targeted Statistical Potentials for Protein-Ligand Interactions. Proteins: Struct, Funct, Bioinf 2005, 61(2):272-287.
45. Velec HFG, Gohlke H, Klebe G. DrugScoreCSD - Knowledge-Based Scoring Function Derived from Small Molecule Crystal Data with Superior Recognition Rate of Near-Native Ligand Poses and Better Affinity Prediction. J Med Chem 2005, 48(20):6296-6303. 10.1021/jm050436v, 16190756.
46. Gohlke H, Hendlich M, Klebe G. Knowledge-Based Scoring Function to Predict Protein-Ligand Interactions. J Mol Biol 2000, 295(2):337-356. 10.1006/jmbi.1999.3371, 10623530.
47. Muegge I. PMF Scoring Revisited. J Med Chem 2006, 49(20):5895-5902. 10.1021/jm050038s, 17004705.
48. Muegge I. Effect of Ligand Volume Correction on PMF Scoring. J Comput Chem 2001, 22(4):418-425.
49. Muegge I. A Knowledge-Based Scoring Function for Protein-Ligand Interactions: Probing the Reference State. Perspect Drug Discov Des 2000, 20:99-114.
50. Muegge I, Martin YC. A General and Fast Scoring Function for Protein-Ligand Interactions: A Simplified Potential Approach. J Med Chem 1999, 42(5):791-804. 10.1021/jm980536j, 10072678.
51. Huang S-Y, Zou X. An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function. J Comput Chem 2006, 27(15):1876-1882. 10.1002/jcc.20505, 16983671.
52. Huang S-Y, Zou X. An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials. J Comput Chem 2006, 27(15):1866-1875. 10.1002/jcc.20504, 16983673.
53. Teramoto R, Fukunishi H. Consensus Scoring with Feature Selection for Structure-Based Virtual Screening. J Chem Inf Model 2008, 48(2):288-295. 10.1021/ci700239t, 18229906.
54. Teramoto R, Fukunishi H. Supervised Scoring Models with Docked Ligand Conformations for Structure-Based Virtual Screening. J Chem Inf Model 2007, 47(5):1858-1867. 10.1021/ci700116z, 17685604.
55. Seifert MHJ. Targeted scoring functions for virtual screening. Drug Discov Today 2009, 14(11-12):562-569. 10.1016/j.drudis.2009.03.013, 19508918.
56. Pfeffer P, Gohlke H. DrugScoreRNA-Knowledge-Based Scoring Function To Predict RNA-Ligand Interactions. J Chem Inf Model 2007, 47(5):1868-1876. 10.1021/ci700134p, 17705464.
57. Antes I, Merkwirth C, Lengauer T. POEM: Parameter Optimization Using Ensemble Methods: Application to Target Specific Scoring Functions. J Chem Inf Model 2005, 45(5):1291-1302. 10.1021/ci050036g, 16180906.
58. Seifert MHJ. Optimizing the Signal-to-Noise Ratio of Scoring Functions for Protein-Ligand Docking. J Chem Inf Model 2008, 48(3):602-612. 10.1021/ci700345n, 18293951.
59. Cheng T, Zhao Y, Li X, Lin F, Xu Y, Zhang X, Li Y, Wang R, Lai L. Computation of Octanol-Water Partition Coefficients by Guiding an Additive Model with Knowledge. J Chem Inf Model 2007, 47(6):2140-2148. 10.1021/ci700257y, 17985865.
60. Kuhne R, Ebert R-U, Schuurmann G. Model Selection Based on Structural Similarity-Method Description and Application to Water Solubility Prediction. J Chem Inf Model 2006, 46(2):636-641. 10.1021/ci0503762, 16562993.
61. Chen J, Lai L. Pocket v.2: Further Developments on Receptor-Based Pharmacophore Modeling. J Chem Inf Model 2006, 46(6):2684-2691. 10.1021/ci600246s, 17125208.
62. Wang R, Gao Y, Lai L. LigBuilder: A Multi-Purpose Program for Structure-Based Drug Design. J Mol Model 2000, 6(7):498-516.
63. Bron C, Kerbosch J. Algorithm 457: Finding All Cliques of an Undirected Graph. Commun ACM 1973, 16(9):575-577.
64. Willett P, Barnard JM, Downs GM. Chemical Similarity Searching. J Chem Inf Comput Sci 1998, 38(6):983-996.
65. Wang R, Fang X, Lu Y, Yang CY, Wang S. The PDBbind Database: Methodologies and Updates. J Med Chem 2005, 48(12):4111-4119. 10.1021/jm048957q, 15943484.
66. Wang R, Fang X, Lu Y, Wang S. The PDBbind Database: Collection of Binding Affinities for Protein-Ligand Complexes with Known Three-Dimensional Structures. J Med Chem 2004, 47(12):2977-2980. 10.1021/jm030580l, 15163179.
67. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucl Acids Res 2000, 28(1):235-242. 10.1093/nar/28.1.235, 102472, 10592235.
68. Zhao Y, Cheng T, Wang R. Automatic Perception of Organic Molecules Based on Essential Structural Information. J Chem Inf Model 2007, 47(4):1379-1385. 10.1021/ci700028w, 17530839.
69. The Sybyl Software (version 7.2). 2006, Tripos Inc.: St. Louis, MO.
70. The Discovery Studio software (version 2.0). 2001, Accelrys Software Inc.: San Diego, CA 92121 USA.
71. Baroni M, Cruciani G, Sciabola S, Perruccio F, Mason JS. A Common Reference Framework for Analyzing/Comparing Proteins and Ligands. Fingerprints for Ligands And Proteins (FLAP): Theory and Application. J Chem Inf Model 2007, 47(2):279-294. 10.1021/ci600253e, 17381166.
72. Marcou G, Rognan D. Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints. J Chem Inf Model 2007, 47(1):195-207. 10.1021/ci600342e, 17238265.
73. Martin EJ, Sullivan DC. AutoShim: Empirically Corrected Scoring Functions for Quantitative Docking with a Crystal Structure and IC50 Training Data. J Chem Inf Model 2008, 48(4):861-872. 10.1021/ci7004548, 18380449.